<tool id="getWigDistance" name="get WIG distance">
    <description>Compute the average data around some genomic coordinates using WIG files (thus covering a large proportion of the genome).</description>
	<requirements>
		<requirement type="set_environment">PYTHONPATH</requirement>
	</requirements>
    <command interpreter="python">
		../Java/Python/getWigDistance.py -i $inputGff3File -f gff3 -w $inputWigFile -a 0.0 -d $distance $strand -o $outputFile
	</command>
	
    <inputs>
    	<param name="inputGff3File" type="data" label="Input Gff3 File" format="gff3"/>
   		<param name="inputWigFile" type="data" label="Input Wig File" format="wig"/>
		<param name="distance" type="integer" value="1000" label="Distance around positions."/>
		<param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Consider both strands separately."/>    
    </inputs>
        
    <outputs>
       	<data name="outputFile" format="png" label="[get WIG distance] PNG output file"/>    
    </outputs> 

	<help>
Plots the average data contained in a set of WIG files (please consult http://genome.ucsc.edu/goldenPath/help/wiggle.html to know more about this format) around the first nucleotides of a annotation file.

The tool needs an transcript list, some WIG files, and a distance. For each transcript, it collects all the values around its first nucleotide, the radius being given by the distance. Then, it computes the average value for each position. A point (*x*, *y*) means that the average value in the WIG file for a nucleotide distant by *x* nucleotides from the first nucleotide of an input transcript is *y*.

You can possibly use a log scale for the *y*-axis.
	</help>
</tool>